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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAAGGACGGGGAAGGGGGAGACGCTGTGACGGGCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctaccacttctctcgctgtctgtcctgcctctgcctgtcgtgccgttgcgtgcgtcaatgctgctgcgcgcggctattgcgcttcaactggttcc...

Basic information

species Zea mays
transcript GRMZM2G045330_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045330_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 2
CACAAGGACGGGGAAGGGGGAGACGCTGTGACGGGCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctaccacttctctcgctgtctgtcctgcctctgcctgtcgtgccgttgcgtgcgtcaatgctgctgcgcgcggctattgcgcttcaactggttcc---
 | ||||| | ||  ||||| ||||| |||||||| || ||||||||||||||||||||||| |||||||||||||| |||||||| ||||          ||  | |   | |||    |   ||| || | || |  || |  | |  ||  || |   |||  |||       || ||  |   
AAGAAGGAGGAGGGCGGGGGCGACGCCGTGACGGGTCACATCATCTCCACCACCATCGGCGGCAAGAACGGCGAGCCGAAGCGGgtgagcttttttcggggtctttttggtttctgttcttctttgt-gtacagtggaatgtgctagttttggcgcccttcgct--tgcttccttgctcgtaacaat
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211462454|gb|FL214396.1|FL214396
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|211467507|gb|FL214416.1|FL214416
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         AACATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|211464982|gb|FL214406.1|FL214406
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|211464984|gb|FL214408.1|FL214408
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|211462452|gb|FL214394.1|FL214394
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|211462450|gb|FL214392.1|FL214392
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|211464973|gb|FL214397.1|FL214397
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|211464986|gb|FL214410.1|FL214410
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|211464978|gb|FL214402.1|FL214402
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGN                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|148936144|gb|EC880210.2|EC880210
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|211464987|gb|FL214411.1|FL214411
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|148955335|gb|EC900888.2|EC900888
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|211462449|gb|FL214391.1|FL214391
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|71433254|gb|DR814304.1|DR814304
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|211464979|gb|FL214403.1|FL214403
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|211462451|gb|FL214393.1|FL214393
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|211467508|gb|FL214417.1|FL214417
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|211462444|gb|FL214386.1|FL214386
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|148971177|gb|EE022031.2|EE022031
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|211467504|gb|FL214413.1|FL214413
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGT                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
EST: gi|148962923|gb|EE013859.2|EE013859
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCA
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCA
EST: gi|211464985|gb|FL214409.1|FL214409
EST:     GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGG                         ACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC
genomic: GCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 226

CACAAGGACGGGGAAGGGGGAGACGCTGTGACGGGCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATCGTCTTCCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 96

CACAAGGACGGGGAAGGGGGAGACGCTGTGACGGGCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATCGTCTTCCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 69

CACAAGGACGGGGAAGGGGGAGACGCTGTGACGGGCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATCGTCTTCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 103

CACAAGGACGGGGAAGGGGGAGACGCTGTGACGGGCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctacc ... ttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATCGTCTTCCAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACAAGGACGGGGAAGGGGGAGACGCTGTGACGGGCCATATCATCTCCACCACCATCGGCGGGAAGAACGGCGAGCCCAAGCGGgtaagctaccacttctctcgctgtctgtcctgcctctgcctgtcgtgccgttgcgtgcgtcaatgctgctgcgcgcggctattgcgcttcaactggttcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
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